Funding & Acknowledgements

The data used in this analysis is from the Export Standardized Tables in the SEACAR Data Discovery Interface (DDI). Documents and information available through the SEACAR DDI are owned by the data provider(s) and users are expected to provide appropriate credit following accepted citation formats. Users are encouraged to access data to maximize utilization of gained knowledge, reducing redundant research and facilitating partnerships and scientific innovation.

With respect to documents and information available from SEACAR DDI, neither the State of Florida nor the Florida Department of Environmental Protection makes any warranty, expressed or implied, including the warranties of merchantability and fitness for a particular purpose arising out of the use or inability to use the data, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.

This report was funded in part, through a grant agreement from the Florida Department of Environmental Protection, Florida Coastal Management Program, by a grant provided by the Office for Coastal Management under the Coastal Zone Management Act of 1972, as amended, National Oceanic and Atmospheric Administration. The views, statements, findings, conclusions and recommendations expressed herein are those of the author(s) and do not necessarily reflect the views of the State of Florida, NOAA or any of their sub agencies.

Published: 2025-07-02

Threshold Filtering

Threshold filters, following the guidance of Florida Department of Environmental Protection’s (FDEP) Division of Environmental Assessment and Restoration (DEAR) are used to exclude specific results values from the SEACAR Analysis. Based on the threshold filters, Quality Assurance / Quality Control (QAQC) Flags are inserted into the SEACAR_QAQCFlagCode and SEACAR_QAQC_Description columns of the export data. The Include column indicates whether the QAQC Flag will also indicate that data are excluded from analysis. No data are excluded from the data export, but the analysis scripts can use the Include column to exclude data (1 to include, 0 to exclude).

Continuous Water Quality threshold values
Parameter Name Units Low Threshold High Threshold
Dissolved Oxygen mg/L -0.000001 50
Dissolved Oxygen Saturation % -0.000001 500
Salinity ppt -0.000001 70
Turbidity NTU -0.000001 4000
Water Temperature Degrees C -5.000000 45
pH None 2.000000 14
Discrete Water Quality threshold values
Parameter Name Units Low Threshold High Threshold
Ammonia, Un-ionized (NH3) mg/L - -
Ammonium, Filtered (NH4) mg/L - -
Chlorophyll a, Corrected for Pheophytin ug/L - -
Chlorophyll a, Uncorrected for Pheophytin ug/L - -
Colored Dissolved Organic Matter PCU - -
Dissolved Oxygen mg/L -0.000001 25
Dissolved Oxygen Saturation % -0.000001 310
Fluorescent Dissolved Organic Matter QSE - -
Light Extinction Coefficient m^-1 - -
NO2+3, Filtered mg/L - -
Nitrate (NO3) mg/L - -
Nitrite (NO2) mg/L - -
Nitrogen, organic mg/L - -
Phosphate, Filtered (PO4) mg/L - -
Salinity ppt -0.000001 70
Secchi Depth m 0.000001 50
Specific Conductivity mS/cm 0.005000 100
Total Kjeldahl Nitrogen mg/L - -
Total Nitrogen mg/L - -
Total Nitrogen mg/L - -
Total Phosphorus mg/L - -
Total Suspended Solids mg/L - -
Turbidity NTU - -
Water Temperature Degrees C 3.000000 40
pH None 2.000000 13
Quality Assurance Flags inserted based on threshold checks listed in Table 1 and 2
SEACAR QAQC Description Include SEACAR QAQCFlagCode
Exceeds maximum threshold 0 2Q
Below minimum threshold 0 4Q
Within threshold tolerance 1 6Q
No defined thresholds for this parameter 1 7Q

Value Qualifiers

Value qualifier codes included within the data are used to exclude certain results from the analysis. The data are retained in the data export files, but the analysis uses the Include column to filter the results.

STORET and WIN value qualifier codes

Value qualifier codes from STORET and WIN data are examined with the database and used to populate the Include column in data exports.

Value Qualifier codes excluded from analysis
Qualifier Source Value Qualifier Include MDL Description
STORET-WIN H 0 0 Value based on field kit determination; results may not be accurate
STORET-WIN J 0 0 Estimated value
STORET-WIN V 0 0 Analyte was detected at or above method detection limit
STORET-WIN Y 0 0

Discrete Water Quality Value Qualifiers

The following value qualifiers are highlighted in the Discrete Water Quality section of this report. An exception is made for Program 476 - Charlotte Harbor Estuaries Volunteer Water Quality Monitoring Network and data flagged with Value Qualifier H are included for this program only.

H - Value based on field kit determiniation; results may not be accurate. This code shall be used if a field screening test (e.g., field gas chromatograph data, immunoassay, or vendor-supplied field kit) was used to generate the value and the field kit or method has not been recognized by the Department as equivalent to laboratory methods.

I - The reported value is greater than or equal to the laboratory method detection limit but less than the laboratory practical quantitation limit.

Q - Sample held beyond the accepted holding time. This code shall be used if the value is derived from a sample that was prepared or analyzed after the approved holding time restrictions for sample preparation or analysis.

S - Secchi disk visible to bottom of waterbody. The value reported is the depth of the waterbody at the location of the Secchi disk measurement.

U - Indicates that the compound was analyzed for but not detected. This symbol shall be used to indicate that the specified component was not detected. The value associated with the qualifier shall be the laboratory method detection limit. Unless requested by the client, less than the method detection limit values shall not be reported

Systemwide Monitoring Program (SWMP) value qualifier codes

Value qualifier codes from the SWMP continuous program are examined with the database and used to populate the Include column in data exports. SWMP Qualifier Codes are indicated by QualifierSource=SWMP.

SWMP Value Qualifier codes
Qualifier Source Value Qualifier Include Description
SWMP -1 1 Optional parameter not collected
SWMP -2 0 Missing data
SWMP -3 0 Data rejected due to QA/QC
SWMP -4 0 Outside low sensor range
SWMP -5 0 Outside high sensor range
SWMP 0 1 Passed initial QA/QC checks
SWMP 1 0 Suspect data
SWMP 2 1 Reserved for future use
SWMP 3 1
SWMP 4 1 Historical: Pre-auto QA/QC
SWMP 5 1 Corrected data

Water Column

The water column habitat extends from the water’s surface to the bottom sediments, and it’s where fish, dolphins, crabs and people swim! So much life makes its home in the water column that the health of marine and coastal ecosystems, as well as human economies, depend on the condition of this vulnerable habitat. Local patterns of rainfall, temperature, winds and currents can rapidly change the condition of the water column, while global influences such as El Niño/La Niña, large-scale fluctuation in sea temperatures and climate change can have long-term effects. Inputs from the prosperity of our day-to-day lives including farming, mining and forestry, and emissions from power generation, automobiles and water treatment can also alter the health of the water column. Acting alone or together, each input can have complex and lasting effects on habitats and ecosystems.


SEACAR evaluates water column health with several essential parameters. These include nutrient surveys of nitrogen and phosphorus, and water quality assessments of salinity, dissolved oxygen, pH, and water temperature. Water clarity is evaluated with Secchi depth, turbidity, levels of chlorophyll a, total suspended solids, and colored dissolved organic matter. Additionally, the richness of nekton is indicated by the abundance of free-swimming fishes and macroinvertebrates like crabs and shrimps.

Seasonal Kendall-Tau Analysis

Indicators must have a minimum of five to ten years, depending on the habitat, of data within the geographic range of the analysis to be included in the analysis. Ten years of data are required for discrete parameters, and five years of data are required for continuous parameters. If there are insufficient years of data, the number of years of data available will be noted and labeled as “insufficient data to conduct analysis”. Further, for the preferred Seasonal Kendall-Tau test, there must be data from at least two months in common across at least two consecutive years within the RCP managed area being analyzed. Values that pass both of these tests will be included in the analysis and be labeled as Use_In_Analysis = TRUE. Any that fail either test will be excluded from the analyses and labeled as Use_In_Analysis = FALSE. The points for all Water Column plots displayed in this section are monthly averages. Trend significance will be denoted as “Significant Trend” (when p < 0.05), or “Non-significant Trend” (when p >= 0.05). Any parameters with insufficient data to perform Seasonal Kendall-Tau test will have their monthly averages plotted without a corresponding trend line.

Water Quality - Discrete

The following files were used in the discrete analysis:

  • Combined_WQ_WC_NUT_Chlorophyll_a_corrected_for_pheophytin-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Chlorophyll_a_uncorrected_for_pheophytin-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Colored_dissolved_organic_matter_CDOM-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Dissolved_Oxygen-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Dissolved_Oxygen_Saturation-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_pH-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Salinity-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Secchi_Depth-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Total_Nitrogen-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Total_Phosphorus-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Total_Suspended_Solids_TSS-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Turbidity-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_Water_Temperature-2025-Mar-06.txt

Chlorophyll a, Corrected for Pheophytin - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average levels of chlorophyll a, corrected for pheophytin, over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only laboratory-analyzed chlorophyll a (triangles) is included in the plot.
Scatter plot of monthly average levels of chlorophyll a, corrected for pheophytin, over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only laboratory-analyzed chlorophyll a (triangles) is included in the plot.
Seasonal Kendall-Tau Trend Analysis for Chlorophyll a, Corrected for Pheophytin
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab No significant trend 2209 15 2002 - 2024 4.1 0.0567 3.084 0.0323 0.3307

Chlorophyll a, corrected for pheophytin, showed no detectable trend between 2002 and 2024.

Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Chlorophyll a, Corrected for Pheophytin
ProgramID N_Data YearMin YearMax
354 2029 2012 2024
5002 212 2002 2024
303 3 2022 2023

Program names:

303 - River, Estuary and Coastal Observing Network1
354 - Rookery Bay National Estuarine Research Reserve System-Wide Monitoring Program2
5002 - Florida STORET / WIN3

Chlorophyll a, Uncorrected for Pheophytin - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average levels of chlorophyll a, uncorrected for pheophytin, over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only laboratory-analyzed chlorophyll a (triangles) is included in the plot.
Scatter plot of monthly average levels of chlorophyll a, uncorrected for pheophytin, over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only laboratory-analyzed chlorophyll a (triangles) is included in the plot.
Seasonal Kendall-Tau Trend Analysis for Chlorophyll a, Uncorrected for Pheophytin
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab Significantly increasing trend 5345 31 1994 - 2024 4.4 0.3358 3.5724 0.0992 0

Monthly average chlorophyll a, uncorrected for pheophytin, increased by 0.1 µg/L per year, indicating a decrease in water clarity.

Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Chlorophyll a, Uncorrected for Pheophytin
ProgramID N_Data YearMin YearMax
354 7218 2002 2024
509 2746 1994 2008
514 413 2001 2017
5002 173 2001 2024
103 35 2021 2021
118 1 2010 2010

Program names:

103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4
118 - National Aquatic Resource Surveys, National Coastal Condition Assessment5
354 - Rookery Bay National Estuarine Research Reserve System-Wide Monitoring Program2
509 - SERC Water Quality Monitoring Network6
514 - Florida LAKEWATCH Program7
5002 - Florida STORET / WIN3

Colored Dissolved Organic Matter - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average colored dissolved organic matter (CDOM) over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only laboratory-analyzed CDOM (triangles) is included in the plot.
Scatter plot of monthly average colored dissolved organic matter (CDOM) over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only laboratory-analyzed CDOM (triangles) is included in the plot.
Seasonal Kendall-Tau Trend Analysis for Colored Dissolved Organic Matter
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab No significant trend 193 12 2001 - 2017 8 0.3619 5.6154 0.2778 0.1533

Colored dissolved organic matter showed no detectable trend between 2001 and 2017.

Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Colored Dissolved Organic Matter
ProgramID N_Data YearMin YearMax
514 193 2001 2017

Program names:

514 - Florida LAKEWATCH Program7

Dissolved Oxygen - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average dissolved oxygen over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only dissolved oxygen values measured in the field (circles) are included in the plot.
Scatter plot of monthly average dissolved oxygen over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only dissolved oxygen values measured in the field (circles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Dissolved Oxygen
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Field Significantly decreasing trend 15353 35 1989 - 2024 5.8 -0.1257 6.1775 -0.0163 0.0006

Monthly average dissolved oxygen decreased by 0.02 mg/L per year.

Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Dissolved Oxygen
ProgramID N_Data YearMin YearMax
509 5403 1994 2008
5002 5170 1989 2024
4043 2975 1999 2020
354 1651 2002 2023
95 442 1997 2018
103 80 2021 2021
572 27 1998 2005
69 22 2001 2001
118 10 2015 2021

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program8
95 - Harmful Algal Bloom Marine Observation Network9
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4
118 - National Aquatic Resource Surveys, National Coastal Condition Assessment5
354 - Rookery Bay National Estuarine Research Reserve System-Wide Monitoring Program2
509 - SERC Water Quality Monitoring Network6
572 - Rookery Bay National Estuarine Research Reserve Seagrass Monitoring10
4043 - RBNERR Fish Assessment11
5002 - Florida STORET / WIN3

Dissolved Oxygen Saturation - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average dissolved oxygen saturation over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only dissolved oxygen saturation values measured in the field (circles) are included in the plot.
Scatter plot of monthly average dissolved oxygen saturation over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only dissolved oxygen saturation values measured in the field (circles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Dissolved Oxygen Saturation
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Field No significant trend 1402 25 1998 - 2024 78 -0.0882 78.9552 -0.2391 0.1253

Dissolved oxygen saturation showed no detectable trend between 1998 and 2024.

Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Dissolved Oxygen Saturation
ProgramID N_Data YearMin YearMax
354 1582 2002 2024
5002 255 2015 2024
572 27 1998 2005
95 1 2008 2008
303 1 2023 2023

Program names:

95 - Harmful Algal Bloom Marine Observation Network9
303 - River, Estuary and Coastal Observing Network1
354 - Rookery Bay National Estuarine Research Reserve System-Wide Monitoring Program2
572 - Rookery Bay National Estuarine Research Reserve Seagrass Monitoring10
5002 - Florida STORET / WIN3

pH - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average pH over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only pH values measured in the field (circles) are included in the plot.
Scatter plot of monthly average pH over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only pH values measured in the field (circles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for pH
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Field Significantly decreasing trend 7368 38 1955 - 2024 7.86 -0.2239 8.1282 -0.006 0

Monthly average pH decreased by 0.01 pH units per year.

Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for pH
ProgramID N_Data YearMin YearMax
5002 4127 1989 2024
509 1719 2001 2008
354 1400 2002 2024
95 514 1955 2018
103 103 2021 2021
69 22 2001 2001
303 1 2023 2023

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program8
95 - Harmful Algal Bloom Marine Observation Network9
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4
303 - River, Estuary and Coastal Observing Network1
354 - Rookery Bay National Estuarine Research Reserve System-Wide Monitoring Program2
509 - SERC Water Quality Monitoring Network6
5002 - Florida STORET / WIN3

Salinity - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average salinity over time. If the time series included ten or more years of discrete observations, significant (blue) or non-significant (magenta) trend lines are also shown. Discrete salinity values derived from grab samples analyzed in the field (circles) or the laboratory (triangles) are both included in the plot.
Scatter plot of monthly average salinity over time. If the time series included ten or more years of discrete observations, significant (blue) or non-significant (magenta) trend lines are also shown. Discrete salinity values derived from grab samples analyzed in the field (circles) or the laboratory (triangles) are both included in the plot.
Seasonal Kendall-Tau Trend Analysis for Salinity
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
All Significantly decreasing trend 16814 53 1954 - 2024 32.7 -0.1588 34.3313 -0.0459 0

Monthly average salinity decreased by 0.05 ppt per year.

Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Salinity
ProgramID N_Data YearMin YearMax
509 5387 1994 2008
5002 5161 1989 2024
4043 3045 1999 2020
354 1929 2002 2024
95 1890 1954 2018
572 31 1998 2005
69 22 2001 2001
118 8 2015 2021
303 1 2023 2023

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program8
95 - Harmful Algal Bloom Marine Observation Network9
118 - National Aquatic Resource Surveys, National Coastal Condition Assessment5
303 - River, Estuary and Coastal Observing Network1
354 - Rookery Bay National Estuarine Research Reserve System-Wide Monitoring Program2
509 - SERC Water Quality Monitoring Network6
572 - Rookery Bay National Estuarine Research Reserve Seagrass Monitoring10
4043 - RBNERR Fish Assessment11
5002 - Florida STORET / WIN3

Secchi Depth - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average Secchi depth over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Secchi depth is only measured in the field (circles).
Scatter plot of monthly average Secchi depth over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Secchi depth is only measured in the field (circles).
Seasonal Kendall-Tau Trend Analysis for Secchi Depth
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Field Significantly increasing trend 768 21 1998 - 2024 -1.0668 0.2564 -1.221 0.0189 0.0002

Monthly average Secchi depth became shallower by 0.02 m per year, indicating a decrease in water clarity.

Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Secchi Depth
ProgramID N_Data YearMin YearMax
5002 409 2006 2024
514 252 2001 2017
103 76 2021 2021
69 22 2001 2001
572 9 1998 2003

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program8
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4
514 - Florida LAKEWATCH Program7
572 - Rookery Bay National Estuarine Research Reserve Seagrass Monitoring10
5002 - Florida STORET / WIN3

Total Nitrogen - Discrete

Total Nitrogen Calculation:

The logic for calculated Total Nitrogen was provided by Kevin O’Donnell and colleagues at FDEP (with the help of Jay Silvanima, Watershed Monitoring Section). The following logic is used, in this order, based on the availability of specific nitrogen components.

  1. TN = TKN + NO3O2;
  2. TN = TKN + NO3 + NO2;
  3. TN = ORGN + NH4 + NO3O2;
  4. TN = ORGN + NH4 + NO2 + NO3;
  5. TN = TKN + NO3;
  6. TN = ORGN + NH4 + NO3;

Additional Information:

  • Rules for use of sample fraction:
    • Florida Department of Environmental Protection (FDEP) report that if both “Total” and “Dissolved” components are reported, only “Total” is used. If the total is not reported, then the dissolved components are used as a best available replacement.
    • Total nitrogen calculations are done using nitrogen components with the same sample fraction, nitrogen components with mixed total/dissolved sample fractions are not used. In other words, total nitrogen can be calculated when TKN and NO3O2 are both total sample fractions, or when both are dissolved sample fractions. Future calculations of total nitrogen values may be based on components with mixed sample fractions.
  • Values inserted into data:
    • ParameterName = “Total Nitrogen”
    • SEACAR_QAQCFlagCode = “1Q”
    • SEACAR_QAQC_Description = “SEACAR Calculated”

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average total nitrogen over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only nitrogen values obtained from laboratory analyses (triangles) are included in the plot.
Scatter plot of monthly average total nitrogen over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only nitrogen values obtained from laboratory analyses (triangles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Total Nitrogen
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab No significant trend 5321 34 1989 - 2024 0.3184 0.0176 0.3751 0.0006 0.7234

Total nitrogen showed no detectable trend between 1989 and 2024.

Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Total Nitrogen
ProgramID N_Data YearMin YearMax
509 2758 1994 2008
5002 1135 1989 2024
354 1051 2002 2018
514 605 2001 2017
303 3 2022 2023

Program names:

303 - River, Estuary and Coastal Observing Network1
354 - Rookery Bay National Estuarine Research Reserve System-Wide Monitoring Program2
509 - SERC Water Quality Monitoring Network6
514 - Florida LAKEWATCH Program7
5002 - Florida STORET / WIN3

Total Phosphorus - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average total phosphorus over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only phosphorus values obtained from laboratory analyses (triangles) are included in the plot.
Scatter plot of monthly average total phosphorus over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only phosphorus values obtained from laboratory analyses (triangles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Total Phosphorus
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab No significant trend 5570 31 1994 - 2024 0.04 0.0728 0.0445 0.0001 0.0537

Total phosphorus showed no detectable trend between 1994 and 2024.

Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Total Phosphorus
ProgramID N_Data YearMin YearMax
509 2735 1994 2008
354 1507 2002 2024
5002 679 2001 2024
514 597 2001 2017
103 96 2021 2021
303 3 2022 2023

Program names:

103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4
303 - River, Estuary and Coastal Observing Network1
354 - Rookery Bay National Estuarine Research Reserve System-Wide Monitoring Program2
509 - SERC Water Quality Monitoring Network6
514 - Florida LAKEWATCH Program7
5002 - Florida STORET / WIN3

Total Suspended Solids - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average total suspended solids (TSS) over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only TSS values obtained from laboratory analyses (triangles) are included in the plot.
Scatter plot of monthly average total suspended solids (TSS) over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only TSS values obtained from laboratory analyses (triangles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Total Suspended Solids
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab Significantly increasing trend 861 31 1989 - 2024 8 0.3785 -1.0549 0.2789 0

Monthly average total suspended solids increased by 0.28 mg/L per year, indicating a decrease in water clarity.

Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Total Suspended Solids
ProgramID N_Data YearMin YearMax
354 1085 2016 2024
5002 359 1989 2017

Program names:

354 - Rookery Bay National Estuarine Research Reserve System-Wide Monitoring Program2
5002 - Florida STORET / WIN3

Turbidity - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average turbidity over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only turbidity values measured in the laboratory (triangles) are included in the plot.
Scatter plot of monthly average turbidity over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only turbidity values measured in the laboratory (triangles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Turbidity
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Lab Significantly increasing trend 6383 32 1989 - 2024 4.365 0.2084 4.5298 0.0888 0

Monthly average turbidity increased by 0.09 NTU per year, indicating a decrease in water clarity.

Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Turbidity
ProgramID N_Data YearMin YearMax
5002 3652 1989 2024
509 2746 1994 2008
354 734 2002 2006
103 92 2021 2021
572 4 2000 2003
95 3 2003 2011
303 1 2023 2023

Program names:

95 - Harmful Algal Bloom Marine Observation Network9
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4
303 - River, Estuary and Coastal Observing Network1
354 - Rookery Bay National Estuarine Research Reserve System-Wide Monitoring Program2
509 - SERC Water Quality Monitoring Network6
572 - Rookery Bay National Estuarine Research Reserve Seagrass Monitoring10
5002 - Florida STORET / WIN3

Water Temperature - Discrete

Seasonal Kendall-Tau Trend Analysis

Scatter plot of monthly average water temperature over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only water temperature measurements taken in the field (circles) are included in the plot.
Scatter plot of monthly average water temperature over time. If the time series included ten or more years of discrete observations, a significant (blue) or non-significant (magenta) trend line is also shown. Only water temperature measurements taken in the field (circles) are included in the plot.
Seasonal Kendall-Tau Trend Analysis for Water Temperature
Activity Type Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
Field Significantly increasing trend 16851 50 1954 - 2024 26.65 0.1045 25.4611 0.0123 0.0018

Monthly average water temperature increased by 0.01°C per year.

Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of discrete water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Programs contributing data for Water Temperature
ProgramID N_Data YearMin YearMax
5002 5654 1989 2024
509 5387 1994 2008
4043 3038 1999 2020
354 1806 2002 2024
95 1336 1954 2018
103 103 2021 2021
572 30 1998 2005
69 22 2001 2001
303 1 2023 2023

Program names:

69 - Fisheries-Independent Monitoring (FIM) Program8
95 - Harmful Algal Bloom Marine Observation Network9
103 - EPA STOrage and RETrieval Data Warehouse (STORET)/WQX4
303 - River, Estuary and Coastal Observing Network1
354 - Rookery Bay National Estuarine Research Reserve System-Wide Monitoring Program2
509 - SERC Water Quality Monitoring Network6
572 - Rookery Bay National Estuarine Research Reserve Seagrass Monitoring10
4043 - RBNERR Fish Assessment11
5002 - Florida STORET / WIN3

Water Quality - Continuous

The following files were used in the continuous analysis:

  • Combined_WQ_WC_NUT_cont_Dissolved_Oxygen_SW-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_Dissolved_Oxygen_Saturation_SW-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_pH_SW-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_Salinity_SW-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_Turbidity_SW-2025-Mar-06.txt

  • Combined_WQ_WC_NUT_cont_Water_Temperature_SW-2025-Mar-06.txt

Continuous monitoring locations in Rookery Bay National Estuarine Research Reserve

Station overview for Continuous parameters by Program
ProgramID ProgramLocationID Years of Data Use in Analysis Parameters
7 02291330 4 FALSE Sal , TempW
7 255123081321300 11 TRUE Sal , TempW
7 255138081321701 9 TRUE Sal , TempW
7 255432081303900 20 TRUE Sal , TempW
7 255443081314700 5 FALSE Sal , TempW
7 255532081314300 3 FALSE Sal , TempW
7 255534081324000 19 TRUE Sal , TempW
7 255654081350200 19 TRUE Sal , TempW
7 255732081363700 5 TRUE Sal , TempW
354 rkbbmwq 2 FALSE DO , DOS , pH , Sal , Turb , TempW
354 rkbfbwq 24 TRUE DO , DOS , pH , Sal , Turb , TempW
354 rkbfuwq 24 TRUE DO , DOS , pH , Sal , Turb , TempW
354 rkblhwq 24 TRUE DO , DOS , pH , Sal , Turb , TempW
354 rkbmbwq 25 TRUE DO , DOS , pH , Sal , Turb , TempW
354 rkbpbwq 9 TRUE DO , DOS , pH , Sal , Turb , TempW
354 rkbuhwq 5 TRUE DO , DOS , pH , Sal , Turb , TempW

Program names:

7 - National Water Information System12
354 - Rookery Bay National Estuarine Research Reserve System-Wide Monitoring Program2

Map showing continuous water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. Sites marked as Use In Analysis (green) are featured in this report.
Map showing continuous water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. Sites marked as Use In Analysis (green) are featured in this report.

Dissolved Oxygen - Continuous

Scatter plot of monthly average dissolved oxygen over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average dissolved oxygen over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for Dissolved Oxygen - All Stations
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
rkbfbwq No significant trend 570320 22 2002 - 2025 5.4 -0.06 5.21 -0.01 0.19
rkbfuwq Significantly decreasing trend 605519 21 2002 - 2025 5.1 -0.32 5.25 -0.03 0
rkbbmwq Insufficient data to calculate trend 10441 2 1997 - 1998 7.2 - - - -
rkblhwq No significant trend 570691 21 2001 - 2024 5.5 0 5.48 0 0.86
rkbmbwq Significantly decreasing trend 613238 22 2000 - 2024 4.4 -0.26 4.89 -0.02 0
rkbpbwq Significantly decreasing trend 289726 9 2016 - 2024 4.9 -0.18 5.21 -0.03 0.02
rkbuhwq No significant trend 58164 5 1996 - 2000 3.6 0.01 3.9 -0.02 1

At three program locations, monthly average dissolved oxygen decreased between 0.02 and 0.03 mg/L per year. No detectable change in monthly average dissolved oxygen was observed at three locations. There was insufficient data to fit a model for one location.

Map showing location of dissolved oxygen continuous water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of dissolved oxygen continuous water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Dissolved Oxygen Saturation - Continuous

Scatter plot of monthly average dissolved oxygen saturation over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average dissolved oxygen saturation over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for Dissolved Oxygen Saturation - All Stations
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
rkbfbwq No significant trend 574626 22 2002 - 2025 78.7 -0.01 78.85 -0.02 0.79
rkbbmwq Insufficient data to calculate trend 10441 2 1997 - 1998 102.4 - - - -
rkbfuwq Significantly decreasing trend 605778 21 2002 - 2025 72.4 -0.25 77.54 -0.24 0
rkblhwq No significant trend 583009 21 2001 - 2024 81.7 0.02 80.58 0.02 0.55
rkbpbwq Significantly decreasing trend 291357 9 2016 - 2024 72.3 -0.18 77.6 -0.36 0.03
rkbmbwq Significantly decreasing trend 619562 22 2000 - 2024 65.1 -0.23 73.35 -0.29 0
rkbuhwq No significant trend 58164 5 1996 - 2000 49.7 0 50.53 -0.02 1

At three program locations, monthly average dissolved oxygen saturation decreased between 0.24 and 0.36% per year. No detectable change in monthly average dissolved oxygen saturation was observed at three locations. There was insufficient data to fit a model for one location.

Map showing location of dissolved oxygen saturation continuous water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of dissolved oxygen saturation continuous water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

pH - Continuous

Scatter plot of monthly average pH over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average pH over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for pH - All Stations
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
rkbfbwq No significant trend 637095 24 2002 - 2025 7.8 0.05 7.82 0 0.23
rkbbmwq Insufficient data to calculate trend 12610 2 1997 - 1998 8.0 - - - -
rkbfuwq No significant trend 660818 24 2002 - 2025 7.7 -0.01 7.71 0 0.79
rkblhwq Significantly increasing trend 629829 24 2001 - 2024 7.9 0.14 7.83 0 0
rkbmbwq Significantly decreasing trend 683502 25 2000 - 2024 7.7 -0.09 7.7 0 0.03
rkbpbwq Significantly increasing trend 283219 9 2016 - 2024 7.8 0.2 7.77 0.01 0.02
rkbuhwq Significantly increasing trend 65814 5 1996 - 2000 7.2 0.37 7.05 0.07 0.01

At three program locations, monthly average pH increased between less than 0.01 and 0.07 pH units per year. At one program location, monthly average pH decreased by less than 0.01 pH units per year. No detectable change in monthly average pH was observed at two locations. There was insufficient data to fit a model for one location.

Map showing location of ph continuous water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of ph continuous water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Salinity - Continuous - Program 7

Scatter plot of monthly average salinity over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average salinity over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for Salinity - Program 7
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
255532081314300 Insufficient data to calculate trend 902 3 2009 - 2011 31 - - - -
255534081324000 Significantly decreasing trend 5789 18 2007 - 2025 32 -0.12 34.52 -0.14 0.02
255654081350200 No significant trend 5802 18 2007 - 2025 32 -0.09 33.97 -0.09 0.08
255732081363700 No significant trend 1434 5 2011 - 2015 34 0.25 32.15 0.52 0.1
02291330 Insufficient data to calculate trend 1697 4 2011 - 2014 35 - - - -
255443081314700 Insufficient data to calculate trend 1465 4 2007 - 2011 32 - - - -
255432081303900 Significantly decreasing trend 6087 19 2006 - 2025 21 -0.2 28.63 -0.25 0
255138081321701 No significant trend 2608 9 2017 - 2025 31 -0.04 31.04 -0.04 0.69
255123081321300 Significantly decreasing trend 1809 8 2007 - 2017 32 -0.23 35.11 -0.44 0.02

At one program location, monthly average salinity increased by 2.06 ppt per year. At five program locations, monthly average salinity decreased between 0.08 and 0.44 ppt per year. No detectable change in monthly average salinity was observed at six locations. There was insufficient data to fit a model for four locations.

Salinity - Continuous - Program 354

Scatter plot of monthly average salinity over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average salinity over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for Salinity - Program 354
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
rkbfbwq No significant trend 669593 24 2002 - 2025 29.6 -0.03 31.48 -0.03 0.47
rkbbmwq Insufficient data to calculate trend 12256 2 1997 - 1998 34.5 - - - -
rkbfuwq No significant trend 686073 24 2002 - 2025 26.0 -0.06 28.81 -0.07 0.15
rkbmbwq Significantly decreasing trend 694825 25 2000 - 2024 33.3 -0.12 34.97 -0.08 0
rkblhwq Significantly decreasing trend 657842 24 2001 - 2024 33.1 -0.16 34.68 -0.1 0
rkbpbwq No significant trend 290041 9 2016 - 2024 30.2 -0.01 30.6 -0.04 0.92
rkbuhwq Significantly increasing trend 68446 5 1996 - 2000 21.1 0.31 16.74 2.06 0.04

At one program location, monthly average salinity increased by 2.06 ppt per year. At five program locations, monthly average salinity decreased between 0.08 and 0.44 ppt per year. No detectable change in monthly average salinity was observed at six locations. There was insufficient data to fit a model for four locations.

Map showing location of salinity continuous water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of salinity continuous water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Turbidity - Continuous

Scatter plot of monthly average turbidity over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average turbidity over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for Turbidity - All Stations
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
rkbfbwq Significantly decreasing trend 649336 24 2002 - 2025 7 -0.39 11.61 -0.24 0
rkbbmwq Insufficient data to calculate trend 10654 2 1997 - 1998 11 - - - -
rkbfuwq Significantly decreasing trend 626788 24 2002 - 2025 6 -0.2 8.53 -0.08 0
rkblhwq Significantly decreasing trend 605017 24 2001 - 2024 8 -0.27 12.4 -0.2 0
rkbmbwq Significantly decreasing trend 670439 25 2000 - 2024 9 -0.22 12.74 -0.13 0
rkbpbwq Significantly decreasing trend 286433 9 2016 - 2024 10 -0.37 13.71 -0.51 0
rkbuhwq No significant trend 61608 5 1996 - 2000 5 -0.11 8.57 -0.7 0.52

At five program locations, monthly average turbidity decreased between 0.08 and 0.51 NTU per year. No detectable change in monthly average turbidity was observed at one location. There was insufficient data to fit a model for one location.

Map showing location of turbidity continuous water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of turbidity continuous water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Water Temperature - Continuous - Program 7

Scatter plot of monthly average water temperature over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average water temperature over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for Water Temperature - Program 7
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
255443081314700 Insufficient data to calculate trend 2011 4 2007 - 2011 29.30 - - - -
255532081314300 Insufficient data to calculate trend 906 3 2009 - 2011 29.30 - - - -
255534081324000 Significantly increasing trend 5845 18 2007 - 2025 26.60 0.14 25.59 0.03 0.01
255654081350200 Significantly increasing trend 5840 18 2007 - 2025 26.75 0.14 26.29 0.04 0.01
255732081363700 No significant trend 1435 5 2011 - 2015 28.40 0.24 27.3 0.23 0.11
02291330 Insufficient data to calculate trend 1901 4 2011 - 2014 28.30 - - - -
255432081303900 Significantly increasing trend 6146 19 2006 - 2025 27.00 0.16 26.21 0.05 0
255123081321300 No significant trend 1818 8 2007 - 2017 27.30 0.1 26.46 0.03 0.38
255138081321701 No significant trend 2626 9 2017 - 2025 27.00 0.07 26.85 0.03 0.55

At seven program locations, monthly average water temperature increased between 0.03 and 0.07°C per year. No detectable change in monthly average water temperature was observed at five locations. There was insufficient data to fit a model for four locations.

Water Temperature - Continuous - Program 354

Scatter plot of monthly average water temperature over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Scatter plot of monthly average water temperature over time at continuously monitored program locations. Each location is analyzed separately, with significant (blue) or non-significant (magenta) trend lines shown for time series that included five or more years of observations.
Seasonal Kendall-Tau Results for Water Temperature - Program 354
Station Statistical Trend Sample Count Years with Data Period of Record Median tau Sen Intercept Sen Slope p
rkbfbwq Significantly increasing trend 685432 24 2002 - 2025 27.0 0.23 26.15 0.04 0
rkbbmwq Insufficient data to calculate trend 12610 2 1997 - 1998 23.8 - - - -
rkbfuwq Significantly increasing trend 696504 24 2002 - 2025 26.9 0.26 26.07 0.07 0
rkblhwq Significantly increasing trend 688994 24 2001 - 2024 27.0 0.25 26.12 0.05 0
rkbmbwq Significantly increasing trend 718152 25 2000 - 2024 26.9 0.26 25.95 0.05 0
rkbpbwq No significant trend 292925 9 2016 - 2024 27.6 0.14 27.03 0.06 0.07
rkbuhwq No significant trend 68971 5 1996 - 2000 26.8 -0.01 26.3 -0.01 1

At seven program locations, monthly average water temperature increased between 0.03 and 0.07°C per year. No detectable change in monthly average water temperature was observed at five locations. There was insufficient data to fit a model for four locations.

Map showing location of water temperature continuous water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of water temperature continuous water quality sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Submerged Aquatic Vegetation

The data file used is: All_SAV_Parameters-2025-Mar-06.txt

Submerged aquatic vegetation (SAV) refers to plants and plant-like macroalgae species that live entirely underwater. The two primary categories of SAV inhabiting Florida estuaries are benthic macroalgae and seagrasses. They often grow together in dense beds or meadows that carpet the seafloor. Macroalgae include multicellular species of green, red and brown algae that often live attached to the substrate by a holdfast. They tend to grow quickly and can tolerate relatively high nutrient levels, making them a threat to seagrasses and other benthic habitats in areas with poor water quality. In contrast, seagrasses are grass-like, vascular, flowering plants that are attached to the seafloor by extensive root systems. Seagrasses occur throughout the coastal areas of Florida, including protected bays and lagoons as well as deeper offshore waters on the continental shelf. Seagrasses have taken advantage of the broad, shallow shelf and clear water to produce two of the most extensive seagrass beds anywhere in continental North America.

Parameters

Percent Cover measures the fraction of an area of seafloor that is covered by SAV, usually estimated by evaluating multiple small areas of seafloor. Percent cover is often estimated for total SAV, individual types of vegetation (seagrass, attached algae, drift algae) and individual species.

Frequency of Occurrence was calculated as the number of times a taxon was observed in a year divided by the number of sampling events, multiplied by 100. Analysis is conducted at the quadrat level and is inclusive of all quadrats (i.e., quadrats evaluated using Braun-Blanquet, modified Braun-Blanquet, and percent cover.”

Species

Turtle grass (Thalassia testudinum) is the largest of the Florida seagrasses, with longer, thicker blades and deeper root structures than any of the other seagrasses. It is considered a climax seagrass species.

Shoal grass (Halodule wrightii) is an early colonizer of vegetated areas and usually grows in water too shallow for other species except widgeon grass. It can often tolerate larger salinity ranges than other seagrass species. Shoal grass is characterized by thin, flat blades, that are narrower than turtle grass blades.

Manatee grass (Syringodium filiforme) is easily recognizable because its leaves are thin and cylindrical instead of the flat, ribbon-like form shared by many other seagrass species. The leaves can grow up to half a meter in length. Manatee grass is usually found in mixed seagrass beds or small, dense monospecific patches.

Widgeon grass (Ruppia maritima) grows in both fresh and salt water and is widely distributed throughout Florida’s estuaries in less saline areas, particularly in inlets along the east coast. This species resembles shoal grass in certain environments but can be identified by the pointed tips of its leaves.

Three species of Halophila spp. are found in Florida - Star grass (Halophila engelmannii), Paddle grass (Halophila decipiens), and Johnson’s seagrass (Halophila johnsonii). These are smaller, more fragile seagrasses than other Florida species and are considered ephemeral. They grow along a single long rhizome, with short blades. These species are not well-studied, although surveys are underway to define their ecological roles.

Notes

Star grass, Paddle grass, and Johnson’s seagrass will be grouped together and listed as Halophila spp. in the following managed areas. This is because several surveys did not specify to the species level:

  • Banana River Aquatic Preserve

  • Indian River-Malabar to Vero Beach Aquatic Preserve

  • Indian River-Vero Beach to Ft. Pierce Aquatic Preserve

  • Jensen Beach to Jupiter Inlet Aquatic Preserve

  • Loxahatchee River-Lake Worth Creek Aquatic Preserve

  • Mosquito Lagoon Aquatic Preserve

  • Biscayne Bay Aquatic Preserve

  • Florida Keys National Marine Sanctuary

Maps showing the temporal scope of SAV sampling sites within the boundaries of Rookery Bay National Estuarine Research Reserve by Program name.
Maps showing the temporal scope of SAV sampling sites within the boundaries of Rookery Bay National Estuarine Research Reserve by Program name.

Click here to view spatio-temporal plots on GitHub.

Sampling locations by Program:

Map showing SAV sampling sites within the boundaries of Rookery Bay National Estuarine Research Reserve. The point size reflects the number of samples at a given sampling site.
Map showing SAV sampling sites within the boundaries of Rookery Bay National Estuarine Research Reserve. The point size reflects the number of samples at a given sampling site.
Program Information for Submerged Aquatic Vegetation
ProgramID N-Data YearMin YearMax method Sample Locations
572 1220 1998 2005 Percent Cover 6

Program names:

572 - Rookery Bay National Estuarine Research Reserve Seagrass Monitoring10

Scatter plots of median percent cover of submerged aquatic vegetation over time by group. Plots for time series that included five or more years of observations show the estimated trend as a blue line.
Scatter plots of median percent cover of submerged aquatic vegetation over time by group. Plots for time series that included five or more years of observations show the estimated trend as a blue line.
Trends in median percent cover for various seagrass species in Rookery Bay National Estuarine Research Reserve - simplified
Trends in median percent cover for various seagrass species in Rookery Bay National Estuarine Research Reserve - simplified
Percent Cover Trend Analysis for Rookery Bay National Estuarine Research Reserve
CommonName Trend Significance (0.05) Period of Record LME-Intercept LME-Slope p
Shoal grass No significant trend 1998 - 2005 33.6288441 -1.7091190 0.2546081
Paddle grass No significant trend 1998 - 2005 -0.4445638 0.0784246 0.3562778
Star grass No significant trend 1998 - 2005 3.5304862 -0.2323271 0.4437138
Manatee grass No significant trend 1998 - 2005 16.1047980 -1.1343869 0.4000887
Turtle grass No significant trend 1998 - 2005 36.9897733 -3.1381134 0.0666614
Total seagrass Significantly decreasing trend 1998 - 2005 68.3694828 -4.5209704 0.0166198

An annual decrease in percent cover was observed for total seagrass (-4.5%). Manatee grass, paddle grass, shoal grass, star grass, and turtle grass showed no detectable change in percent cover.

Frequency of occurrence for various seagrass species in Rookery Bay National Estuarine Research Reserve
Frequency of occurrence for various seagrass species in Rookery Bay National Estuarine Research Reserve

SAV Water Column Analysis

The following parameters are available for Rookery Bay National Estuarine Research Reserve within the SAV_WC_Report:

  • Colored Disolved Organic Matter

  • Chlorophyll a

  • Dissolved Oxygen

  • Dissolved Oxygen Saturation

  • pH

  • Salinity

  • Secchi Depth

  • Water Temperature

  • Total Nitrogen

  • Total Suspended Solids

  • Turbidity

Access the reports here: DRAFT_SAV_WC_Report_2024-11-20.pdf

Nekton

The data file used is: All_NEKTON_Parameters-2025-Mar-06.txt

Bar graph(s) of annual average nekton richness over time for species groups occurring in at least 1% of samples. The bar colors represent species groups including bony fishes, cartilaginous fishes, decapod crustaceans (e.g., shrimps, crabs, and lobsters), and cephalopods (e.g., squid). Gear types and sizes are indicated in the panel label.
Bar graph(s) of annual average nekton richness over time for species groups occurring in at least 1% of samples. The bar colors represent species groups including bony fishes, cartilaginous fishes, decapod crustaceans (e.g., shrimps, crabs, and lobsters), and cephalopods (e.g., squid). Gear types and sizes are indicated in the panel label.
Nekton Species Richness
Gear Type Sample Count Number of Years Period of Record Median N of Taxa Mean N of Taxa
Trawl (6.1) 6071 20 1999 - 2020 0.27 0.63

The median annual number of taxa was 0.27 based on 6,071 observations collected by 6.1-meter trawl between 1999 and 2020.

Map showing location of nekton sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.
Map showing location of nekton sampling locations within the boundaries of Rookery Bay National Estuarine Research Reserve. The bubble size on the maps above reflect the amount of data available at each sampling site.

Species list

Acanthostracion quadricornis2 Eugerres plumieri2 Mugil spp.2
Achirus lineatus2 Floridichthys carpio2 Mycteroperca microlepis2
Albula vulpes2 Ginglymostoma cirratum2 Myrophis punctatus2
Aluterus schoepfii2 Gobiesox strumosus2 Nicholsina usta2
Anarchopterus criniger2 Gobionellus oceanicus2 Ogcocephalus cubifrons2
Anchoa spp.2 Gobiosoma bosc2 Ogilbia cayorum2
Ancylopsetta quadrocellata2 Gobiosoma robustum2 Oligoplites saurus2
Archosargus probatocephalus2 Gunterichthys longipenis2 Opisthonema oglinum2
Archosargus rhomboidalis2 Gymnura micrura2 Opsanus beta2
Ariopsis felis2 Halodule wrightii1 Orthopristis chrysoptera2
Bagre marinus2 Halophila decipiens1 Paralichthys albigutta2
Bairdiella chrysoura2 Halophila engelmannii1 Penaeus spp.2
Brevoortia smithi2 Harengula jaguana2 Pogonias cromis2
Brevoortia spp.2 Hippocampus erectus2 Prionotus scitulus2
Calamus arctifrons2 Hippocampus zosterae2 Prionotus tribulus2
Callinectes sapidus2 Hoplosternum littorale2 Rachycentron canadum2
Caranx spp.2 Hypanus americanus2 Rhinoptera bonasus2
Caulerpa spp.1 Hypanus sabinus2 Sciaenops ocellatus2
Centropomus undecimalis2 Hyporhamphus unifasciatus2 Scorpaena brasiliensis2
Chaetodipterus faber2 Hypostomus plecostomus2 Selene vomer2
Chasmodes saburrae2 Hypsoblennius hentz2 Serraniculus pumilio2
Chilomycterus schoepfii2 Lagodon rhomboides2 Sphoeroides nephelus2
Chloroscombrus chrysurus2 Leiostomus xanthurus2 Sphoeroides spengleri2
Cichlidae spp.2 Lepomis spp.2 Sphyraena guachancho2
Citharichthys macrops2 Leptocephalus larvae2 Stephanolepis hispida2
Citharichthys spilopterus2 Lophogobius cyprinoides2 Symphurus plagiusa2
Clupeidae2 Lucania parva2 Syngnathus louisianae2
Ctenogobius boleosoma2 Lutjanus analis2 Syngnathus scovelli2
Ctenogobius smaragdus2 Lutjanus griseus2 Synodus foetens2
Cynoscion arenarius2 Lutjanus synagris2 Syringodium filiforme1
Cynoscion nebulosus2 Menippe mercenaria2 Thalassia testudinum1
Diplectrum formosum2 Menticirrhus spp.2 Total seagrass1
Echeneis neucratoides2 Microgobius gulosus2 Trachinotus falcatus2
Elops saurus2 Microgobius thalassinus2 Trinectes maculatus2
Epinephelus itajara2 Micropterus salmoides2 Urophycis floridana2
Etropus crossotus2 Monacanthus ciliatus2 Acanthostracion quadricornis2
Eucinostomus spp.2 Mugil cephalus2 Achirus lineatus2

1 - Submerged Aquatic Vegetation, 2 - Nekton

References

1.
Sanibel-Captiva Conservation Foundation (SCCF). River, Estuary and Coastal Observing Network. (2024).
2.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Rookery Bay National Estuarine Research Reserve. Rookery Bay National Estuarine Research Reserve System-Wide Monitoring Program. (2024).
3.
Florida Department of Environmental Protection (DEP). Florida STORET / WIN. (2024).
4.
U.S. Environmental Protection Agency (EPA). EPA STOrage and RETrieval Data Warehouse (STORET)/WQX. (2023).
5.
U.S. Environmental Protection Agency (EPA); Office of Water; National Oceanic and Atmospheric Administration (NOAA); U.S. Geological Survey (USGS); U.S. Fish and Wildlife Service (USFWS); National Estuary Program (NEP); coastal states. National Aquatic Resource Surveys, National Coastal Condition Assessment. (2021).
6.
Florida International University (FIU); Southeastern Environmental Research Program. SERC Water Quality Monitoring Network. (2008).
7.
University of Florida (UF); Institute of Food and Agricultural Sciences. Florida LAKEWATCH Program. (2024).
8.
Florida Fish and Wildlife Conservation Commission (FWC). Fisheries-Independent Monitoring (FIM) Program. (2022).
9.
Florida Fish and Wildlife Conservation Commission (FWC); Florida Fish and Wildlife Research Institute (FWRI). Harmful Algal Bloom Marine Observation Network. (2018).
10.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Rookery Bay National Estuarine Research Reserve. Rookery Bay National Estuarine Research Reserve Seagrass Monitoring. (2005).
11.
Florida Department of Environmental Protection (DEP); Office of Resilience and Coastal Protection (RCP); Rookery Bay National Estuarine Research Reserve. RBNERR Fish Assessment. (2023).
12.
U.S. Geological Survey (USGS). National Water Information System. (2024).